Hi, what ever interior urethra pain you had before and what your having now is not related to the affair since you wore a condom and no germs could get inside. Just impossible to happen and they cant get inside the condom to cause an infection either. Most likely the constant masturbating is causing your issues.
All i can suggest is to have a doc swabbed the inside and have a PCR test performed to see if any DNA show up.
On a side note, masturbating inside a sock, its possible some of the fabric got inside causing a urinary track infection.
So I'm sitting here and March of 2016 and I still have urethra pain. I've been tested again for Gon, Cly, Syph, herp, and still all negative. Lol I can laugh about it now because I feel like it's just apart of my life now. Protected sex, all these symptoms but no positives. Maybe urethra scar tissue? I'm thinking I had a STI and it's been cured. Maybe just aftermath.
I think you need to move onto investigating prostate, kidney and bladder issues.
Have an ultrasound scheduled
Ended up getting a MRI done. Doc said everything looked normal. For over a year now I've had regular penis pain daily with no discharge. Does not burn when I pee but I have urethral irritation afterwards. I've developed a small raised portion of my penis opening on the left side. Is not painful to the touch and does not have a lesion or any sort of puss/drainage or even a head to it. I'm confused and out of ideas. No discharge, small raised bump that has been there for over 3 months, pain in urethra.